Mass Effect Trilogy: The 15 toughest story decisions

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Mar 21, 2017

Mass Effect: Andromeda, BioWare's highly-anticipated follow-up to their Mass Effect video game trilogy, has finally been released. The game allows fans to once again enter the Mass Effect universe, which captivated players with its gripping storyline where their choices—for the most part—left a major impact. In the original trilogy, these were often difficult to make and determined everything from the fate of whole races to, sometimes, the fate of close friends.

As we prepare to see if Andromeda will provide that same level of choice in its story, I wanted to look back at the decisions that were the most challenging during the first three games. I revisited my canon play-through with a colonist sole survivor FemShep vanguard and crafted a list of the 15 decisions I think were the toughest to make in the series. Here's my list counting down to the hardest decision along with the ultimate choice I made in my play-through for each.

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Knock out or kill the Zhu's Hope colonists (Mass Effect)

During the mission on Feros, it turns out the Thorian is controlling the Zhu's Hope colonists and to get to the Thorian, Commander Shepard and her squad need to go through the colony. This presents a problem since the Thorian will instruct the colonists to attack you with the help of its creepers as you try to reach it. Do you just go in guns blazing and kill the colonists along with the Thorian's creepers even though it's not really the colonists' fault? It's certainly the most direct and least time-consuming option, but there is an alternative. You can equip your grenades with anti-Thorian gas and use them to knock the colonists out. This is more difficult since you have a limited number of grenades and you need to be smart about using them so they don't run out. You can find a few more in the colony, but if you use them all and some colonists remain the only other way to knock them out is to melee attack them. A helpful counter on the bottom of the screen tells you how many of the 16 colonists are still alive as you go through so you either know how well you're doing using the grenades or how many more you have to take out before it's all over. Should Shepard take the extra time and effort to save as many colonists as she can or just plow through to get straight to the Thorian?

My choice: Knock out the colonists

While this is not the toughest of the tough decisions, it's certainly one from the game that's extremely frustrating to me. I try to make sure everyone survives since I play a bit more paragon in the first game whereas if I'm renegade, I don't care about their lives at all. So the initial decision is easy. However, for me at least, trying to follow through on doing the right thing is really annoying. Every. Time. I almost always run out of grenades because aiming them just right can be a pain and one always bounces off something to explode somewhere useless! Then trying to melee them usually leads to one member of my squad dying, because I told them not to shoot the colonists but the colonists are shooting them and at least one companion for some reason never stays in cover. After a few minutes of this, it gets quite tempting to just stop trying. Still ... I remind myself it's not the colonists' fault that they're attacking and resist the urge to start killing them even if I'm the last one from my squad standing at the end.

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Who will represent humanity on the Council (Mass Effect)

After the fighting is over and Saren and Sovereign are defeated in Mass Effect, Commander Shepard has one last choice to make. Whether or not the Council survives, humanity will be a part of it moving forward meaning a councilor must be chosen. Shepard is asked to recommend someone for the spot. After everything she's done, her suggestion will have considerable weight and basically whoever she backs will get the role. Shepard can recommend Captain Anderson or Ambassador Udina. Udina is a politician who might not be everyone's favorite person and can be selfish, but does care about humanity and knows his way around the political arena. That being said, Anderson is someone Shepard trusts and tends to do what's right no matter what. While not a politician, Anderson also has the military background they might need when the Reapers arrive.

My choice: Captain Anderson

Udina may have the political experience, but the fact that Shepard trusts Anderson matters to me. I think Anderson would be a quick learner and could navigate the political scene easily after a while. He'd put humanity and not himself first, unlike Udina who I could see being interested in political power much more than doing what's right. Plus, after interacting with him in the first game, I just didn't want to put him in such an important powerful position as the first human councilor on the council. With a war coming as well, it made sense to have Anderson on the council since he would know what to do in order to prepare for a fight and believes what Shepard says about the Reapers. He could insist that the council listen to Shepard. Even though we learn later on that despite Anderson's efforts, this doesn't help the council believe in the "Reapers," as the Turian councilor would say, but still. At the time, it seemed like Anderson was the best option!

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Romance option (all games)

This decision may not be as serious as some of the others in the game perhaps. However, you can't tell me it's not difficult! Deciding who to romance in the first game isn't too hard since there are just three options in Kaidan, Ashley and Liara (though it can be tricky choosing between Lirara and either of the two humans.) It's when you reach the other games though that the number of romance-able characters expands and Shepard has some difficult romantic decisions to make. Do you stay true to your Mass Effect romance or start something new with your new crew in Mass Effect 2? By Mass Effect 3, Shepard has even more new potential romantic avenues to explore as well as old romances that return that she can consider continuing. Do you get back together with your companion from the first game? Do you stay with the one from Mass Effect 2 or do you commit to a brand-new person?

My choice: Garrus Vakarian

There's just no Shepard without Vakarian! Best friend, skilled sniper and quite an impressive dancer, this Turian on the Normandy is irresistible. Like Tali, he's been with you through it all from the very beginning and starting a romance in Mass Effect 2 feels like a natural progression of your relationship. It just makes sense after everything you've both been through. He's kind, sweet, tough, a little awkward and honest with you about what he thinks. You may disagree sometimes, but no matter what you have each other's backs. The connection the game lets you develop with the character is, in my opinion, the most emotional of the series. Once I started this romance, there was no going back or changing for me.

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Whether or not to save the Citadel Council (Mass Effect)

In the battle at the end of the first game, Commander Shepard is presented with an important choice regarding the Council. They are unable to escape in their ship, the Destiny Ascension, and need help if they're going to survive. Considering how unhelpful the Asari, Salarian and Turian members of the Council have been throughout the game, their opinions on humanity and the high stakes of the battle, deciding whether or not to help them is difficult. The Alliance fleet is ready to intervene, but saving the Council means the loss of human lives and the fleet won't exactly be good as reinforcements anymore. Instead you can hold the fleet back to wait and then use them to directly attack Sovereign when the opportunity arises. However, in that scenario, the Council dies. The lives of the three councilors, as well as everyone else aboard the Destiny Ascension, are in Shepard's hands.

My choice: Save the Council

In the end, my Shepard couldn't doom the Council and everyone else who was unfortunate enough to be with them to death. They were extremely unhelpful and annoying in the game, but my Shepard was determined to be better than them and to show them humanity can be an important part of the larger galactic community and make a difference. She wanted to be an example of how humanity isn't a selfish species and what better way to do that than by saving the Council's lives? At this point it was also pretty clear humanity couldn't stand alone against the Reapers and the galaxy was going to need to join forces to stop them, so it made sense to take the first step and save the Council.

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Capture Balak or save the hostages (Mass Effect)

In the Bring Down the Sky DLC, Commander Shepard has to stop an asteroid from crashing into the planet Terra Nova. It turns out Batarians are behind the attack and once Shepard stops the asteroid she comes face-to-face with the terrorist leader Balak who presents Shepard with a choice. Balak has a number of hostages locked up and set explosives to detonate. In order to save them, Shepard has to let Balak go. If Shepard tries to attack Balak instead, the hostages will die. There are a few things to consider. If you let Balak go, he might strike again. Who knows how many people might die then, but can you sacrifice the lives of the hostages there then and now to prevent future deaths? Or do you save the hostages and hope the Alliance can stop Balak before something else happens?

My choice: Save the hostages

While I knew almost immediately I couldn't leave the hostages to die, I didn't choose that option right away. I still forced myself to think about the consequences of this action. By letting Balak go, more people might die. I had the chance to stop him right now. At what cost, though? I just couldn't sacrifice Kate and the others if it was in my power to save them. I let Balak go. Ultimately, I'm glad I did too because it saved the hostages and also led to an interesting encounter with the Batarian in Mass Effect 3.

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Rewrite the Geth heretics or destroy them (Mass Effect 2)

During Legion's loyalty mission in Mass Effect 2, Shepard must decide what to do about the Geth heretics. These heretics have adapted a Reaper virus that they want to upload to all Geth that will force them into thinking they should worship the Reapers. Shepard and her team go to stop them, but Legion discovers you can do something other than destroy the heretics. The virus can actually be repurposed to rewrite the heretics instead and make them accept the opinion of Legion and his Geth. It forces a belief on the Geth, but is that an ethical issue if they're just machines? Does it leave the door open for them to somehow betray everyone down the road? Will rewriting them strengthen the entire Geth group, making them a bigger threat? Is killing them the safer route?

My choice: Rewrite the Geth

Shepard learning more about Legion influenced me here. Forming a relationship with the unique Geth showed me that the entire race didn't have to be our enemy. If it was possible to work with Legion and his group of Geth, then why not return these heretics to that friendly group and strengthen a potential ally? They could be an asset in the coming fight against the Reapers if they thought as Legion did. I thought they should at least be given that second chance, even with the possibility of their betrayal in the future, instead of dooming them all to death. Of course, it does feel slightly unethical forcing them to believe one way. I definitely felt guilty about that. However, I thought the positives of rewriting them outweighed the negatives in this case.

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Give the Illusive Man the Collector Base or destroy it (Mass Effect 2)

In the Collector Base, Shepard and her team receive a transmission from the Illusive Man. He tells Shepard that she should set a timed radiation pulse. This will kill the Collectors and leave the base with all its technology intact. The Illusive Man wants to study it to see if that knowledge can be helpful against the Reapers. Shepard can choose to do this or to go through with the original plan of destroying the base, where so many humans lost their lives. However, if the base's technology can help against the Reapers maybe it would make the lives lost at the base have meaning. Would destroying the base honor them or mean they died for nothing?

My choice: Destroy the base

I did not make this decision quickly. I felt a gut instinct towards destroying the base, but I stopped to really consider it. I understand the argument from the other side. The information here could be a great resource against the Reapers and maybe it would mean the people didn’t die for nothing. Perhaps I would have even done it if it wasn't Cerberus and the Illusive Man asking. After everything in the game and the extreme dislike and distrust for the Illusive Man and Cerberus that my Shepard developed, I couldn't believe that the base would just be used to fight the Reapers. I feared the Illusive Man would use it for more than that good cause and then the deaths that happened at the base would be twisted into something worse. I couldn't let that happen, even if it meant losing possible data to help against the Reapers.

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Keep or destroy Maelon's genophage data (Mass Effect 2)

During Mordin's loyalty mission you discover that the student, Maelon, you thought you were rescuing is actually there voluntarily. He performed terrible experiments in order to try to figure out how to cure the genophage, which he regrets being a part of creating. When Mordin's confrontation with Maelon is over, you're left with the option to either keep or destroy his research. It's a difficult decision since the research is the result of all the horrible things Maelon did. Yet, the possibility of it being useful in the future does exist. If they ever want to cure the genophage, the research can come in handy but does keeping it somehow also condone what Maelon did? Or does it, like Mordin says at one point, make the deaths of Maelon's victims mean something instead of nothing?

My choice: Keep the data

I sat and thought about this for quite a while, but finally I encouraged Mordin to keep the data. My Shepard was never really a fan of the genophage and if there was any chance of the data being helpful in curing it at some point I decided the research was worth saving. Maybe it could lead to something good that could act as a memorial for those who lost their lives. I may think it was the right idea, but I'll always feel a little bit bad for keeping it around. In a way, this felt similar to deciding what to do with the Collector Base. The difference was though that I trusted Moridn, and unlike the Illusive Man I believed Mordin would not do anything terrible with the research if we kept it.

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Reveal the Salarian Dalatrass' deal or keep it secret (Mass Effect 3)

Before heading down for the main Tuchanka mission, the Salarian Dalatrass contacts Commander Shepard to try to make a deal. She tells Shepard that the Shroud, which is needed to spread the genophage cure to the Krogan, has been sabotaged. All Shepard has to do in order to have the Salarians' support is not tell anyone about the sabotage, thus leaving the cure to fail. No one else hears this message, but Shepard is given more than one opportunity to reveal the secret sabotage to Wrex or Wreav, Eve, Mordin, and the rest of the team during the mission. Do you reveal the truth at the first opportunity? Hold it back at first, but tell them the second time it comes up? Or do you keep the secret until the last moment or forever in order to make sure the cure doesn't work?

My choice: Wait to tell Mordin until the end

I was surprised by how hesitant I was to reveal the truth when the opportunity arose during this mission. Up until this point I was completely okay with curing the genophage, but the Salarians' offer was tempting and I found myself wondering if I was just dooming the galaxy to a future war if we managed to survive the Reapers, even with Wrex and Eve there to try to keep the Krogan from repeating past mistakes. So every time I was asked if there was anything wrong, I lied. I knew I wanted to cure the genophage, but revealing this offer? It just felt so strange. Until I was alone with Mordin. Maybe I just didn't want to give Wrex and Eve another reason to hate the Salarians. I needed them to work together ultimately, after all. But I felt ashamed, and that was amplified by Mordin's "and you knew" when I told him. Ouch. At least I could admit I was wrong, but still it definitely speaks to how powerful these games are that a conversation decision like this can cause such a reaction from the player!

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Rescue Admiral Koris or the civilians on Rannoch (Mass Effect 3)

During the Quarian attack on Rannoch, Shepard learns that Admiral Koris sacrificed his ship. He crashed on the planet in an escape pod and is now stranded on the planet along with members of his crew, all civilians, who also escaped the ship. After making contact with Koris, he asks you to rescue the civilians and won't tell you where to find him. He's actually cut off from the others and facing approaching Geth, meaning Shepard has to choose who to save: Koris or the civilians. Without Koris' leadership, the Civilian Fleet is considering leaving the flotilla and his voice opposing the war with the Geth will be lost. However, the civilians didn't want the war either and can't fight on their own. Do you leave them or Koris to die?

My choice: Rescue Admiral Koris

Even though I felt terrible leaving the noncombatants at the hands of the Geth, I knew I needed Koris' leadership if I was going to somehow stop the war between the Geth and the Quarians. Since Mass Effect 2, Koris was against going back to Rannoch and believed the Quarians had wronged the Geth. He thought there was the possibility they could coexist, something none of the other Admirals really considered. It was a hard choice to make, but I knew I had to sacrifice the civilians since Koris was needed if there was ever going to be a chance for peace and a chance to save both races.

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Free or kill the Rachni queen (Mass Effect)

On Noveria Shepard discovers a Rachni queen, the last of her kind that the galaxy thought all died in the Rachni Wars. Shepard must decide what to do with this surprise survivor: release her so she can live with her children or kill her. The Rachni queen says if she's allowed to live she wants to teach her children harmony and that she doesn't know what happened in the war. Considering the devastation that happened during the war, letting her live risks the chance that such destruction can return to the galaxy. Killing her though means basically committing genocide since her death would mean the end of the Rachni at last.

My choice: Free her

While once again there's risk involved choosing one decision over another, I chose to free the queen. One reason is because the idea of being responsible for the death of an entire race was just too horrible to consider. Could they all really be so dangerous with no redeeming qualities whatsoever that they deserve to cease existing? Here was a rare second chance after we thought they were already gone forever! However small the chance might be, I wanted to see if the queen could do things differently this time and if showing mercy could make a difference. Also, when she talks about the war it sounds like it wasn’t completely the Rachni's fault and someone else may have been responsible for their actions. This leaves the possibility open that they could fall under this mysterious control again of course, but it also means they might not just want war and could live with the rest of the galaxy peacefully. That was all enough for me to decide to forget the acid and let her go.

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Choosing the Geth or the Quarians on Rannoch, if you can't choose peace (Mass Effect 3)

Once the Geth are free of the Reapers' control, the battle above Rannoch with the Quarians comes to a brief halt. Legion tells you he wants to upload the Reaper code to the other Geth to give them all free will allowing them to help in the fight against the Reapers. Tali argues that uploading the code would lead to her people's destruction. It falls to Shepard to decide who to side with here, knowing that most likely the side Shepard doesn't choose will die. Not only does the fate of two races rest in her hands, but she has a companion on each of these opposing sides. After everything the Geth have been through, and coming to know Legion, how can Shepard destroy them? At the same time, do the Quarians deserve to die now that they're so close to reclaiming their lost homeworld?

My choice: Quarians

While in my canon play-through I go with peace between the two, and I've played both other options depending on my renegade and paragon specific games, if I have to choose something other than peace with my Shepard it pains me to say I'd go with the Quarians. The reason it pains me is because generally I don't like the Quarians very much. I think the Geth deserve to live and it's the Quarians' fault for starting the war in the first place. They're also not exactly nice to Tali half the time. However, I can't let Tali die. That's the only reason I'd choose the Quarians over the Geth. While I love Legion, Tali has been at Shepard's side since the start of this crazy adventure and is one of her best friends. She's been loyal through it all and losing her is just not an option for my Shepard. If only she could live without her people, I'd go with the Geth, but since she can't I unfortunately have to doom Legion and his race.

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Whether or not to cure the genophage (Mass Effect 3)

Finally, in the last game, it seems like there's a chance for the genophage to be cured. The big question is should you do it? By this point Mordin, who helped develop the genophage in the first place and defended it in the previous game, has changed his mind and believes it should be cured. Of course, the Krogan also want it to be cured, but the Salarians keep reminding Shepard of the dangers of doing so. Depending on who is with you, Wrex or Wreav, the danger the Krogan present if they expand again might be more obvious than otherwise. Do you doom a species or potentially doom the galaxy to a war with the Krogan after defeating the Reapers? Do the "what ifs" really justify dooming a whole species anyway? And what about Mordin? All of these choices are given added weight by the emotional conversation you have with the Salarian. Depending on your morality and other decisions you’ve made, his mind might not be easy to change. Do you risk killing him then if he won't go along if you choose to trick the Krogan into believing you cured the genophage when you really didn't?

My choice: Cure the genophage

In the end, I can't let the genophage continue. My Shepard tells Mordin about the sabotage and they discuss how he changed his mind. He admits he made a mistake before, and by the end of that conversation, I just can't say no to him or try to convince him to not go up the tower. That's not to say I wasn't hesitant even after spending the majority of the trilogy thinking a cure was a good thing. The Dalatrass' offer, though, in the midst of everything, made me hesitate since their aid would be extremely helpful and it made me think of all the potential consequences once again. After getting to know Wrex, Eve, Grunt and other Krogans though, I couldn't justify denying them a future. Hopefully everyone would be able to keep from repeating past mistakes. Knowing Mordin would be sacrificing himself to do this didn't make it an easy choice either. I'll admit, I teared up. I sat there as the cure was dispersed and thought of Mordin and the future and was devastated and hopeful at the same time. It was one of the toughest and most emotional moments of the entire game.

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Destroy, Control, Synthesis, or Refuse endings (Mass Effect 3)

There's a lot you can say about the endings, but I'm just going to focus on the fact that you do have to choose at the end of the game even if you don't like them. The options at the end of the game, with the Extended Cut DLC, basically boil down to four. You can choose to destroy the Reapers along with the rest of the machines in the galaxy, or you can control the Reapers. You can also combine synthetic and organic life, merging the two in order to end conflict between them, or you can refuse to pick any of them, making the battle continue and ultimately losing the fight in this cycle. In almost every one, Shepard ceases to be Shepard. The only ending where she survives is one you can get by destroying the Reapers where a scene implies she probably lived. This is a galaxy-changing decision, so what do you do?

My choice: Destroy

After fighting for so long against the Reapers, I just couldn't go with any of the others. That doesn't mean I made it quickly or easily, though. The thought of losing of the Geth, after having them make peace with the Quarians, and Edi, who had become a friend and meant so much to Joker, was dreadful. Could I condemn them to stop the Reapers? Part of me likes to believe it's possible to bring them back and that they're not gone forever after choosing this, but I guess that will just have to remain my head canon since we'll probably never really know. At least the galaxy can rebuild everything else that was destroyed, so they can go on to have a hopefully bright Reaper-free future, and thanks to that brief scene, my Shepard hopefully survived to reunite with her old crew.

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Rescue Ashley or Kaidan on Virmire (Mass Effect)

During the assault on Saren's base, Ashley and Kaidan both find themselves in the middle of trouble. Once you succeed in placing the bomb to destroy the base, the squad mate you sent with Kirrahe contacts you to say they're pinned down by the Geth. The other squad mate tells you to go help while they set up the bomb you're using to destroy the base. As you're on the way to assist, you see a Geth ship heading to where you came from and learn from the squad mate with the bomb that the Geth have arrived. They activate the bomb so no matter what, it will go off. Shepard now can no longer save everyone. She has to choose who to aid. She can continue on and save the squad mate she was on the way to rescue or go back to the bomb and rescue the one that stayed behind. You've come to know these companions and have possibly even romanced one of them. Who do you save and who do you leave behind?

My choice: Kaidan

This tops my list because it happened on such a personal level. It involved two people my Shepard had really come to trust and care about throughout the game. This was personal and I knew the consequences were going to be devastating no matter who I chose because there was no way for me to save both of them. It was going to hurt not only me, but also the other members of my crew. Especially the one that I chose to live. I went with Kaidan because he was the one I was romancing and I knew my Shepard could not ignore those feelings and leave him behind. I also found him to be less annoying than Ashley, who I found hard to like through most of the game though by Virmire I felt we'd arrived at a good place. This was the first major decision in the game that I can remember sitting there thinking about for a really long time. It may not have been one that would impact the whole galaxy, but it was going to impact the Normandy family and that made it the toughest choice of them all.

What choice was the hardest for you to make? Did we leave any decisions off the list that would make your top 15? Tell us in the comments!